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Katsuda T, Sussman JH, Ito K, Katznelson A, Yuan S, Takenaka N, Li J, Merrell AJ, Cure H, Li Q, Rasool RU, Asangani IA, Zaret KS, Stanger BZ. Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity. Nat Commun 2024; 15:1761. [PMID: 38409161 PMCID: PMC10897393 DOI: 10.1038/s41467-024-45939-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.
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Affiliation(s)
- Takeshi Katsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jonathan H Sussman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenji Ito
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Katznelson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Salina Yuan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Naomi Takenaka
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jinyang Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Allyson J Merrell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Hector Cure
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Qinglan Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reyaz Ur Rasool
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Irfan A Asangani
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ben Z Stanger
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Katsuda T, Sussman J, Li J, Merrell AJ, Vostrejs W, Secreto A, Matsuzaki J, Ochiya T, Stanger BZ. Evidence for in vitro extensive proliferation of adult hepatocytes and biliary epithelial cells. Stem Cell Reports 2023; 18:1436-1450. [PMID: 37352852 PMCID: PMC10362498 DOI: 10.1016/j.stemcr.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Over the last several years, a method has emerged that endows adult hepatocytes with in vitro proliferative capacity, producing chemically induced liver progenitors (CLiPs). However, there is a growing controversy regarding the origin of these cells. Here, we provide lineage tracing-based evidence that adult hepatocytes acquire proliferative capacity in vitro using rat and mouse models. Unexpectedly, we also found that the CLiP method allows biliary epithelial cells to acquire extensive proliferative capacity. Interestingly, after long-term culture, hepatocyte-derived cells (hepCLiPs) and biliary epithelial cell-derived cells (bilCLiPs) become similar in their gene expression patterns, and they both exhibit differentiation capacity to form hepatocyte-like cells. Finally, we provide evidence that hepCLiPs can repopulate injured mouse livers, reinforcing our earlier argument that CLiPs can be a cell source for liver regenerative medicine. This study advances our understanding of the origin of CLiPs and motivates the application of this technique in liver regenerative medicine.
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Affiliation(s)
- Takeshi Katsuda
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jonathan Sussman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Jinyang Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Allyson J Merrell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - William Vostrejs
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthony Secreto
- Department of Medicine, Stem Cell and Xenograft Core, University of Pennsylvania, Philadelphia, PA, USA
| | - Juntaro Matsuzaki
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan; Division of Pharmacotherapeutics, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan
| | - Ben Z Stanger
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
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3
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Katsuda T, Sussman J, Ito K, Katznelson A, Yuan S, Li J, Merrell AJ, Takenaka N, Cure H, Li Q, Rasool RU, Asangani IA, Zaret KS, Stanger BZ. Physiological reprogramming in vivo mediated by Sox4 pioneer factor activity. bioRxiv 2023:2023.02.14.528556. [PMID: 36824858 PMCID: PMC9948957 DOI: 10.1101/2023.02.14.528556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.
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Affiliation(s)
- Takeshi Katsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Jonathan Sussman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Kenji Ito
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- The Institute for Regenerative Medicine, University of Pennsylvania Philadelphia, PA
| | - Andrew Katznelson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- The Institute for Regenerative Medicine, University of Pennsylvania Philadelphia, PA
| | - Salina Yuan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Jinyang Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Allyson J. Merrell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Naomi Takenaka
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- The Institute for Regenerative Medicine, University of Pennsylvania Philadelphia, PA
| | - Hector Cure
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Qinglan Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- The Institute for Regenerative Medicine, University of Pennsylvania Philadelphia, PA
| | - Reyaz Ur Rasool
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Irfan A. Asangani
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Kenneth S. Zaret
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- The Institute for Regenerative Medicine, University of Pennsylvania Philadelphia, PA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Ben Z. Stanger
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
- The Institute for Regenerative Medicine, University of Pennsylvania Philadelphia, PA
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4
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Sefton EM, Gallardo M, Tobin CE, Collins BC, Colasanto MP, Merrell AJ, Kardon G. Fibroblast-derived Hgf controls recruitment and expansion of muscle during morphogenesis of the mammalian diaphragm. eLife 2022; 11:e74592. [PMID: 36154712 PMCID: PMC9514848 DOI: 10.7554/elife.74592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 09/13/2022] [Indexed: 12/01/2022] Open
Abstract
The diaphragm is a domed muscle between the thorax and abdomen essential for breathing in mammals. Diaphragm development requires the coordinated development of muscle, connective tissue, and nerve, which are derived from different embryonic sources. Defects in diaphragm development cause the common and often lethal birth defect, congenital diaphragmatic hernias (CDH). HGF/MET signaling is required for diaphragm muscularization, but the source of HGF and the specific functions of this pathway in muscle progenitors and effects on phrenic nerve have not been explicitly tested. Using conditional mutagenesis in mice and pharmacological inhibition of MET, we demonstrate that the pleuroperitoneal folds (PPFs), transient embryonic structures that give rise to the connective tissue in the diaphragm, are the source of HGF critical for diaphragm muscularization. PPF-derived HGF is directly required for recruitment of MET+ muscle progenitors to the diaphragm and indirectly (via its effect on muscle development) required for phrenic nerve primary branching. In addition, HGF is continuously required for maintenance and motility of the pool of progenitors to enable full muscularization. Localization of HGF at the diaphragm's leading edges directs dorsal and ventral expansion of muscle and regulates its overall size and shape. Surprisingly, large muscleless regions in HGF and Met mutants do not lead to hernias. While these regions are likely more susceptible to CDH, muscle loss is not sufficient to cause CDH.
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Affiliation(s)
- Elizabeth M Sefton
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Mirialys Gallardo
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Claire E Tobin
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Brittany C Collins
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Mary P Colasanto
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | | | - Gabrielle Kardon
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
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5
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Merrell AJ, Peng T, Li J, Sun K, Li B, Katsuda T, Grompe M, Tan K, Stanger BZ. Dynamic Transcriptional and Epigenetic Changes Drive Cellular Plasticity in the Liver. Hepatology 2021; 74:444-457. [PMID: 33423324 PMCID: PMC8271088 DOI: 10.1002/hep.31704] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/05/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Following liver injury, a fraction of hepatocytes adopt features of biliary epithelial cells (BECs) in a process known as biliary reprogramming. The aim of this study was to elucidate the molecular events accompanying this dramatic shift in cellular identity. APPROACH AND RESULTS We applied the techniques of bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, and assay for transposase-accessible chromatin with high-throughput sequencing to define the epigenetic and transcriptional changes associated with biliary reprogramming. In addition, we examined the role of TGF-β signaling by profiling cells undergoing reprogramming in mice with hepatocyte-specific deletion in the downstream TGF-β signaling component mothers against decapentaplegic homolog 4 (Smad4). Biliary reprogramming followed a stereotyped pattern of altered gene expression consisting of robust induction of biliary genes and weaker repression of hepatocyte genes. These changes in gene expression were accompanied by corresponding modifications at the chromatin level. Although some reprogrammed cells had molecular features of "fully differentiated" BECs, most lacked some biliary characteristics and retained some hepatocyte characteristics. Surprisingly, single-cell analysis of Smad4 mutant mice revealed a dramatic increase in reprogramming. CONCLUSION Hepatocytes undergo widespread chromatin and transcriptional changes during biliary reprogramming, resulting in epigenetic and gene expression profiles that are similar to, but distinct from, native BECs. Reprogramming involves a progressive accumulation of biliary molecular features without discrete intermediates. Paradoxically, canonical TGF-β signaling through Smad4 appears to constrain biliary reprogramming, indicating that TGF-β can either promote or inhibit biliary differentiation depending on which downstream components of the pathway are engaged. This work has implications for the formation of BECs and bile ducts in the adult liver.
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Affiliation(s)
- Allyson J Merrell
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- These authors contributed equally to this work
| | - Tao Peng
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- These authors contributed equally to this work
| | - Jinyang Li
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Sun
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, PA 19104, USA
| | - Bin Li
- Papé Family Pediatric Research Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - Takeshi Katsuda
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Markus Grompe
- Papé Family Pediatric Research Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - Kai Tan
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben Z. Stanger
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Sela Y, Li J, Kuri P, Merrell AJ, Li N, Lengner C, Rompolas P, Stanger BZ. Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation. eLife 2021; 10:63270. [PMID: 33620315 PMCID: PMC7929558 DOI: 10.7554/elife.63270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer patients often harbor occult metastases, a potential source of relapse that is targetable only through systemic therapy. Studies of this occult fraction have been limited by a lack of tools with which to isolate discrete cells on spatial grounds. We developed PIC-IT, a photoconversion-based isolation technique allowing efficient recovery of cell clusters of any size – including single-metastatic cells – which are largely inaccessible otherwise. In a murine pancreatic cancer model, transcriptional profiling of spontaneously arising microcolonies revealed phenotypic heterogeneity, functionally reduced propensity to proliferate and enrichment for an inflammatory-response phenotype associated with NF-κB/AP-1 signaling. Pharmacological inhibition of NF-κB depleted microcolonies but had no effect on macrometastases, suggesting microcolonies are particularly dependent on this pathway. PIC-IT thus enables systematic investigation of metastatic heterogeneity. Moreover, the technique can be applied to other biological systems in which isolation and characterization of spatially distinct cell populations is not currently feasible.
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Affiliation(s)
- Yogev Sela
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Jinyang Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Paola Kuri
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Dermatology, University of Pennsylvania, Philadelphia, PA, United States
| | - Allyson J Merrell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Ning Li
- Department of Biomedical Sciences, School of Veterinary Medicine, Philadelphia, PA, United States.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Chris Lengner
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biomedical Sciences, School of Veterinary Medicine, Philadelphia, PA, United States.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Pantelis Rompolas
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Dermatology, University of Pennsylvania, Philadelphia, PA, United States
| | - Ben Z Stanger
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, United States.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, United States.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
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7
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Li J, Yuan S, Norgard RJ, Yan F, Sun YH, Kim IK, Merrell AJ, Sela Y, Jiang Y, Bhanu NV, Garcia BA, Vonderheide RH, Blanco A, Stanger BZ. Epigenetic and Transcriptional Control of the Epidermal Growth Factor Receptor Regulates the Tumor Immune Microenvironment in Pancreatic Cancer. Cancer Discov 2020; 11:736-753. [PMID: 33158848 DOI: 10.1158/2159-8290.cd-20-0519] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/09/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
Although immunotherapy has revolutionized cancer care, patients with pancreatic ductal adenocarcinoma (PDA) rarely respond to these treatments, a failure that is attributed to poor infiltration and activation of T cells in the tumor microenvironment (TME). We performed an in vivo CRISPR screen and identified lysine demethylase 3A (KDM3A) as a potent epigenetic regulator of immunotherapy response in PDA. Mechanistically, KDM3A acts through Krueppel-like factor 5 (KLF5) and SMAD family member 4 (SMAD4) to regulate the expression of the epidermal growth factor receptor (EGFR). Ablation of KDM3A, KLF5, SMAD4, or EGFR in tumor cells altered the immune TME and sensitized tumors to combination immunotherapy, whereas treatment of established tumors with an EGFR inhibitor, erlotinib, prompted a dose-dependent increase in intratumoral T cells. This study defines an epigenetic-transcriptional mechanism by which tumor cells modulate their immune microenvironment and highlights the potential of EGFR inhibitors as immunotherapy sensitizers in PDA. SIGNIFICANCE: PDA remains refractory to immunotherapies. Here, we performed an in vivo CRISPR screen and identified an epigenetic-transcriptional network that regulates antitumor immunity by converging on EGFR. Pharmacologic inhibition of EGFR is sufficient to rewire the immune microenvironment. These results offer a readily accessible immunotherapy-sensitizing strategy for PDA.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Jinyang Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Salina Yuan
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert J Norgard
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fangxue Yan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yu H Sun
- Center for RNA Biology, Department of Biochemistry and Biophysics, Department of Biology, University of Rochester Medical Center, Rochester, New York
| | - Il-Kyu Kim
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Allyson J Merrell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yogev Sela
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yanqing Jiang
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Natarajan V Bhanu
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Benjamin A Garcia
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert H Vonderheide
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania.,Institute for Immunology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrés Blanco
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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8
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Yuan S, Natesan R, Sanchez-Rivera FJ, Li J, Bhanu NV, Yamazoe T, Lin JH, Merrell AJ, Sela Y, Thomas SK, Jiang Y, Plesset JB, Miller EM, Shi J, Garcia BA, Lowe SW, Asangani IA, Stanger BZ. Global Regulation of the Histone Mark H3K36me2 Underlies Epithelial Plasticity and Metastatic Progression. Cancer Discov 2020; 10:854-871. [PMID: 32188706 DOI: 10.1158/2159-8290.cd-19-1299] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/19/2020] [Accepted: 03/12/2020] [Indexed: 12/11/2022]
Abstract
Epithelial plasticity, reversible modulation of a cell's epithelial and mesenchymal features, is associated with tumor metastasis and chemoresistance, leading causes of cancer mortality. Although different master transcription factors and epigenetic modifiers have been implicated in this process in various contexts, the extent to which a unifying, generalized mechanism of transcriptional regulation underlies epithelial plasticity remains largely unknown. Here, through targeted CRISPR/Cas9 screening, we discovered two histone-modifying enzymes involved in the writing and erasing of H3K36me2 that act reciprocally to regulate epithelial-to-mesenchymal identity, tumor differentiation, and metastasis. Using a lysine-to-methionine histone mutant to directly inhibit H3K36me2, we found that global modulation of the mark is a conserved mechanism underlying the mesenchymal state in various contexts. Mechanistically, regulation of H3K36me2 reprograms enhancers associated with master regulators of epithelial-to-mesenchymal state. Our results thus outline a unifying epigenome-scale mechanism by which a specific histone modification regulates cellular plasticity and metastasis in cancer. SIGNIFICANCE: Although epithelial plasticity contributes to cancer metastasis and chemoresistance, no strategies exist for pharmacologically inhibiting the process. Here, we show that global regulation of a specific histone mark, H3K36me2, is a universal epigenome-wide mechanism that underlies epithelial-to-mesenchymal transition and mesenchymal-to-epithelial transition in carcinoma cells. These results offer a new strategy for targeting epithelial plasticity in cancer.This article is highlighted in the In This Issue feature, p. 747.
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Affiliation(s)
- Salina Yuan
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ramakrishnan Natesan
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Jinyang Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Natarajan V Bhanu
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taiji Yamazoe
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey H Lin
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Allyson J Merrell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yogev Sela
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stacy K Thomas
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yanqing Jiang
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacqueline B Plesset
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Junwei Shi
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Benjamin A Garcia
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Howard Hughes Medical Institute, New York, New York
| | - Irfan A Asangani
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
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9
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Yuan S, Natesan R, Sanchez-Rivera FJ, Li J, Bhanu NV, Yamazoe T, Lin JH, Merrell AJ, Thomas SK, Shi J, Garcia BA, Lowe SW, Asangani IA, Stanger BZ. Abstract A59: CRISPR screen identifies global regulation of H3K36me2 as an epigenomic mechanism underlying epithelial plasticity in pancreatic ductal adenocarcinoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.panca19-a59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastasis and chemoresistance, the most lethal consequences of cancer progression, are associated with a form of cellular plasticity known as the epithelial-to-mesenchymal transition (EMT). During this process, epithelial cells disassemble their intercellular junctions and acquire morphologic and motile phenotypes reminiscent of fibroblasts. As a form of cell fate change, EMT is likely driven by alterations to the chromatin landscape. Indeed, there is increasing evidence that epigenetic modifiers act at the promoters of key epithelial and mesenchymal genes. However, since much of this evidence is focused on specific, handpicked loci, the true extent to which EMT-mediated transcriptional rewiring depends on epigenetic factors remains largely unexplored. We therefore performed a targeted CRISPR screen in plastic pancreatic ductal adenocarcinoma (PDA) cell lines to unbiasedly identify epigenetic modifiers critical for this process. More specifically, we found that in the absence of the methyltransferase Nsd2, a writer of H3K36me2, our once plastic cells are fixed in the epithelial state, while in the absence of the demethylase Kdm2a, an eraser of H3K36me2, they remain in the mesenchymal state. These genes were also found to have functional implications for invasion and metastasis in PDA. Since loss of Nsd2 and Kdm2a results in global loss and gain of H3K36me2, respectively, we examined the function of the histone mark itself with a mutant histone that can no longer be methylated at K36 (H3K36M). Expression of H3K36M is sufficient to push plastic cells of various cancer types to an epithelial fate, implying that the modification itself, regardless of which writer or eraser is active, is the key regulator of EMT. Furthermore, we performed histone mass spectrometry and found that even without any genetic perturbations, higher global levels of H3K36me2 are indeed associated with the mesenchymal state. Finally, we mapped H3K36me2 across the genome and found that widespread loss of H3K36me2 leads to dramatic alterations in the enhancer landscape, which in turn correlates with the observed transcriptomic changes. While H3K36me2 is known to play important roles in DNA repair and mRNA splicing, our findings demonstrate a novel role for H3K36me2 as a central epigenetic regulator of EMT and metastasis by regulating enhancer activity genome wide. Just as importantly, despite massive changes in global H3K36me2 levels, the cellular phenotypes affected are remarkably specific to cell identity and differentiation. Collectively, these results implicate a novel mechanism by which global epigenomic changes underpin the transcriptional rewiring associated with epithelial plasticity.
Citation Format: Salina Yuan, Ramakrishnan Natesan, Francisco J. Sanchez-Rivera, Jinyang Li, Natarajan V Bhanu, Taiji Yamazoe, Jeffrey H. Lin, Allyson J. Merrell, Stacy K. Thomas, Junwei Shi, Ben A. Garcia, Scott W. Lowe, Irfan A. Asangani, Ben Z. Stanger. CRISPR screen identifies global regulation of H3K36me2 as an epigenomic mechanism underlying epithelial plasticity in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A59.
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Affiliation(s)
- Salina Yuan
- 1University of Pennsylvania, Philadelphia, PA,
| | | | | | - Jinyang Li
- 1University of Pennsylvania, Philadelphia, PA,
| | | | | | | | | | | | - Junwei Shi
- 1University of Pennsylvania, Philadelphia, PA,
| | | | - Scott W. Lowe
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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10
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Li J, Byrne KT, Markosyan N, Yamazoe T, Yan F, Chen Z, Sun YH, Lin J, Sela Y, Norgard RJ, Yuan S, Merrell AJ, Tobias JW, Vonderheide RH, Stanger BZ. Abstract A28: Investigation of tumor-cell-intrinsic factors regulating immune infiltration and response to immunotherapy in pancreatic cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.panca19-a28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Resistance to immunotherapy is one major problem of current clinical care for cancer patients. While T-cell abundance is essential for tumor responsiveness to immunotherapy, factors that dictate T-cell infiltration in tumor microenvironments are not fully understood. To understand the tumor cell-intrinsic factors underlying the heterogeneity of tumor immunity and sensitivity to immunotherapy, we established a new experimental system by generating a library of congenic pancreatic tumor cell clones from a genetic mouse model driven by mutant Kras and p53. These tumor cell clones robustly formed implanted tumors that recapitulated the T cell-inflamed and non-T cell-inflamed tumor microenvironments in human patients, associated with distinct patterns of infiltration by T cells and myeloid cells. We found that the non-T cell-inflamed phenotype was dominant over the T cell-inflamed phenotype in the local tumor microenvironment. Both quantitative and qualitative features, specifically expression of markers of prior TCR activation, of intratumoral CD8+ T cells predicted the response to immunotherapies. An integrated transcriptomic and epigenetic analysis revealed that tumor cell-intrinsic expression of the chemokine CXCL1 as a major determinant of the non-T cell-inflamed microenvironment, and ablation of tumor cell-intrinsic CXCL1 promoted T-cell infiltration and sensitivity to a combination of chemotherapies, CD40 agonist, and checkpoint blockades. Similarly, we identified tumor cell-intrinsic EPHA2 and PTGS2 as key regulators of immune infiltration and immunotherapy response in our experimental system. Ablation of tumor cell-intrinsic EPHA2 or PTGS2 enhanced T-cell infiltration and suppressed myeloid cell infiltration in implanted pancreatic tumors, and increased sensitivities of tumors to the combined immunotherapy. These results demonstrated that heterogeneity of tumor immune phenotypes is driven by tumor cell-intrinsic factors that can be manipulated to influence the outcome of immunotherapies. The observation that non-T cell-inflamed phenotype is dominant emphasized the importance of targeting mechanisms driving T-cell low phenotype for improving immunotherapy response.
Citation Format: Jinyang Li, Katelyn T Byrne, Nune Markosyan, Taiji Yamazoe, Fangxue Yan, Zeyu Chen, Yu H. Sun, Jeffrey Lin, Yogev Sela, Robert J. Norgard, Salina Yuan, Allyson J. Merrell, John W. Tobias, Robert H. Vonderheide, Ben Z. Stanger. Investigation of tumor-cell-intrinsic factors regulating immune infiltration and response to immunotherapy in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A28.
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Affiliation(s)
- Jinyang Li
- 1University of Pennsylvania, Philadelphia, PA,
| | | | | | | | - Fangxue Yan
- 1University of Pennsylvania, Philadelphia, PA,
| | - Zeyu Chen
- 1University of Pennsylvania, Philadelphia, PA,
| | - Yu H. Sun
- 2University of Rochester, Rochester, NY
| | - Jeffrey Lin
- 1University of Pennsylvania, Philadelphia, PA,
| | - Yogev Sela
- 1University of Pennsylvania, Philadelphia, PA,
| | | | - Salina Yuan
- 1University of Pennsylvania, Philadelphia, PA,
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11
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Norgard RJ, Maddipati R, Aiello NM, Balli D, Pitarresi JR, Rosario-Berrios DN, Li J, Yuan S, Yamazoe T, Sela Y, Merrell AJ, Wengyn MD, Sun K, Rustgi AK, Stanger BZ. Abstract B38: Calcium signaling induces a partial EMT in pancreatic ductal adenocarcinoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.panca19-b38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastasis and chemoresistance—the two main reasons for the high mortality of cancer—are associated with a form of cellular plasticity known as epithelial-to-mesenchymal transition (EMT). Cancer cells undergoing EMT become invasive, facilitating metastasis, and undergo a shift in their vulnerability to antineoplastic drugs. In recent work, it has been shown that EMT does not involve a single mechanism but rather a diversity of programs, yielding a continuum of cell phenotypes along the epithelial-mesenchymal spectrum. We previously developed a lineage-traced model of pancreatic ductal adenocarcinoma (PDA) to study EMT in the context of stochastically-arising tumors. As expected, epithelial-mesenchymal plasticity in some tumors involves transcriptional repression of the epithelial state, resulting in a “classical EMT” (C-EMT) phenotype. Surprisingly, however, epithelial-mesenchymal plasticity in the majority of tumors involves post-transcriptional repression of the epithelial state, resulting in a “partial EMT” (P-EMT) phenotype. These two plasticity programs are associated with other aspects of tumor biology as well, including distinct modes of cellular invasion. Here, we identify calcium signaling in pancreatic cancer cells as a regulator of the P-EMT phenotype. Prolonged calcium flux induces PDA cells to remove E-cadherin (ECAD) and other epithelial proteins from the surface and relocalize it intracellularly. This loss of the epithelial phenotype occurs without changes in the abundance of mRNAs for these proteins, reminiscent of the P-EMT phenotype observed in tumors in vivo. In addition, inhibition of the calcium-signaling protein calmodulin blunts this EMT-inducing effect. These results implicate calcium signaling as a mediator of partial EMT phenotypes.
Citation Format: Robert J. Norgard, Ravikanth Maddipati, Nicole M. Aiello, David Balli, Jason R. Pitarresi, Derick N. Rosario-Berrios, Jinyang Li, Salina Yuan, Taiji Yamazoe, Yogev Sela, Allyson J. Merrell, Maximilian D. Wengyn, Kathryn Sun, Anil K. Rustgi, Ben Z. Stanger. Calcium signaling induces a partial EMT in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B38.
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Affiliation(s)
| | | | | | - David Balli
- University of Pennsylvania, Philadelphia, PA
| | | | | | - Jinyang Li
- University of Pennsylvania, Philadelphia, PA
| | - Salina Yuan
- University of Pennsylvania, Philadelphia, PA
| | | | - Yogev Sela
- University of Pennsylvania, Philadelphia, PA
| | | | | | - Kathryn Sun
- University of Pennsylvania, Philadelphia, PA
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12
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Abstract
To maintain proper organ size, nature has devised trans-organ communication systems-involving both paracrine and circulating regulatory factors-to safeguard homeostasis. In this issue of Developmental Cell, Ji et al. (2019) now describe an enterohepatic feedback loop that balances tissue size and function in the mammalian liver.
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Affiliation(s)
- Allyson J Merrell
- Departments of Medicine and Cellular and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben Z Stanger
- Departments of Medicine and Cellular and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Li J, Byrne KT, Yan F, Yamazoe T, Chen Z, Baslan T, Richman LP, Lin JH, Sun YH, Rech AJ, Balli D, Hay CA, Sela Y, Merrell AJ, Liudahl SM, Gordon N, Norgard RJ, Yuan S, Yu S, Chao T, Ye S, Eisinger-Mathason TSK, Faryabi RB, Tobias JW, Lowe SW, Coussens LM, Wherry EJ, Vonderheide RH, Stanger BZ. Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy. Immunity 2018; 49:178-193.e7. [PMID: 29958801 PMCID: PMC6707727 DOI: 10.1016/j.immuni.2018.06.006] [Citation(s) in RCA: 422] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/31/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
The biological and functional heterogeneity between tumors-both across and within cancer types-poses a challenge for immunotherapy. To understand the factors underlying tumor immune heterogeneity and immunotherapy sensitivity, we established a library of congenic tumor cell clones from an autochthonous mouse model of pancreatic adenocarcinoma. These clones generated tumors that recapitulated T cell-inflamed and non-T-cell-inflamed tumor microenvironments upon implantation in immunocompetent mice, with distinct patterns of infiltration by immune cell subsets. Co-injecting tumor cell clones revealed the non-T-cell-inflamed phenotype is dominant and that both quantitative and qualitative features of intratumoral CD8+ T cells determine response to therapy. Transcriptomic and epigenetic analyses revealed tumor-cell-intrinsic production of the chemokine CXCL1 as a determinant of the non-T-cell-inflamed microenvironment, and ablation of CXCL1 promoted T cell infiltration and sensitivity to a combination immunotherapy regimen. Thus, tumor cell-intrinsic factors shape the tumor immune microenvironment and influence the outcome of immunotherapy.
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Affiliation(s)
- Jinyang Li
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Katelyn T Byrne
- Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA.
| | - Fangxue Yan
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Taiji Yamazoe
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Institute for Immunology, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY 10065, USA
| | - Lee P Richman
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Jeffrey H Lin
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Yu H Sun
- Center for RNA Biology, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Andrew J Rech
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - David Balli
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Ceire A Hay
- Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Yogev Sela
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Allyson J Merrell
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Shannon M Liudahl
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Naomi Gordon
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Robert J Norgard
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Salina Yuan
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Sixiang Yu
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Timothy Chao
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Shuai Ye
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - T S Karin Eisinger-Mathason
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - John W Tobias
- Penn Genomic Analysis Core, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, 415 East 68(th) Street New York, NY 10065, USA
| | - Lisa M Coussens
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - E John Wherry
- Abramson Cancer Center, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Robert H Vonderheide
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA.
| | - Ben Z Stanger
- Abramson Family Cancer Research Institute, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA.
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14
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Merrell AJ, Kardon G. Development of the diaphragm -- a skeletal muscle essential for mammalian respiration. FEBS J 2013; 280:4026-35. [PMID: 23586979 DOI: 10.1111/febs.12274] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 12/26/2022]
Abstract
The mammalian diaphragm muscle is essential for respiration, and thus is one of the most critical skeletal muscles in the human body. Defects in diaphragm development leading to congenital diaphragmatic hernias (CDH) are common birth defects and result in severe morbidity or mortality. Given its functional importance and the frequency of congenital defects, an understanding of diaphragm development, both normally and during herniation, is important. We review current knowledge of the embryological origins of the diaphragm, diaphragm development and morphogenesis, as well as the genetic and developmental aetiology of diaphragm birth defects.
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Affiliation(s)
- Allyson J Merrell
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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15
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Mathew SJ, Hansen JM, Merrell AJ, Murphy MM, Lawson JA, Hutcheson DA, Hansen MS, Angus-Hill M, Kardon G. Connective tissue fibroblasts and Tcf4 regulate myogenesis. Development 2011; 138:371-84. [PMID: 21177349 DOI: 10.1242/dev.057463] [Citation(s) in RCA: 231] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Muscle and its connective tissue are intimately linked in the embryo and in the adult, suggesting that interactions between these tissues are crucial for their development. However, the study of muscle connective tissue has been hindered by the lack of molecular markers and genetic reagents to label connective tissue fibroblasts. Here, we show that the transcription factor Tcf4 (transcription factor 7-like 2; Tcf7l2) is strongly expressed in connective tissue fibroblasts and that Tcf4(GFPCre) mice allow genetic manipulation of these fibroblasts. Using this new reagent, we find that connective tissue fibroblasts critically regulate two aspects of myogenesis: muscle fiber type development and maturation. Fibroblasts promote (via Tcf4-dependent signals) slow myogenesis by stimulating the expression of slow myosin heavy chain. Also, fibroblasts promote the switch from fetal to adult muscle by repressing (via Tcf4-dependent signals) the expression of developmental embryonic myosin and promoting (via a Tcf4-independent mechanism) the formation of large multinucleate myofibers. In addition, our analysis of Tcf4 function unexpectedly reveals a novel mechanism of intrinsic regulation of muscle fiber type development. Unlike other intrinsic regulators of fiber type, low levels of Tcf4 in myogenic cells promote both slow and fast myogenesis, thereby promoting overall maturation of muscle fiber type. Thus, we have identified novel extrinsic and intrinsic mechanisms regulating myogenesis. Most significantly, our data demonstrate for the first time that connective tissue is important not only for adult muscle structure and function, but is a vital component of the niche within which muscle progenitors reside and is a critical regulator of myogenesis.
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Affiliation(s)
- Sam J Mathew
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, Utah 84112, USA
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